Contents
Jupyter Notebook files
Use minnie_plotly_and_vtk_visualizer.ipynb
to generate a 2D and 3D interactive views of one or more cells of
interest from the minnie mm^3 volume. Uses matplotlib, plotly, and
vtk/openGL visualization methods. See an example visualization
below.
vtk visualization of neurons in the minnie volume
Use pyvista_decimate_mesh_cell_bodies_minnie.ipynb
to decimate cell meshes from the minnie volume. Default decimation
setting is 95%. You must first download the meshes to your local drive
using the minnie_plotly_and_vtk_visualizer.ipynb notebook.
Decimated files will be saved in the ‘/dec’ subdirectory. Note that
astrocyte meshes may take several hours to decimate. Most other cell
types will only take minutes.
Use vtk_decimated_cell_meshes_minnie.ipynb
to generate a 3D interactive view of one or more cells of interest using
decimated meshes from the minnie mm^3 volume. Uses vtk/openGL and has a
save view function. See an example visualization below.
